Sticker systems with complex structures

 In this paper, we propose a variant of sticker systems which uses molecules with complex structures. Since the original sticker systems (Paun et al. (1998) [2, 8]) working on double strands of DNA have been studied as a formal model for self-assembly in DNA computing, we extend the sticker systems to working on more complex (higher-order) structures of DNA molecules. The advantage of sticker systems with complex structures is that augmented with weak codings we can obtain the characterization of recursively enumerable languages by using only sticking (hybridization) operations for complex molecules, while the usual sticker systems require more complicated operations such as the simultaneous use of couples of dominoes or coherent computations besides morphisms.     

How efficiently can room at the bottom be traded away for speed at the top?

Given exponential 2 ⁿ space, we know that an Adleman-Lipton computation can decide many hard problems – such as boolean formula and boolean circuit evaluation – in a number of steps that is linear in the problem size n. We wish to better understand the process of designing and comparing bio-molecular algorithms that trade away weakly exponential space to achieve as low a running time as possible, and to analyze the efficiency of their space and time utilization relative to those of their best extant classical/bio-molecular counterparts. We propose a randomized framework which augments that of the sticker model of Roweis et al. to provide an abstract setting for analyzing the space-time efficiency of both deterministic and randomized bio-molecular algorithms. We explore its power by developing and analyzing such algorithms for theCovering Code Creation (CCC) and k-SAT problems. In the process, we uncover new classical algorithms for CCC andk-SAT that, while exploiting the same space-time trade-off as the best previously known classical algorithms, are exponentially more efficient than them in terms of space-time product utilization. This work indicates that the proposed abstract bio-molecular setting for randomized algorithm design provides a logical tool of independent interest. This revised version was published online in June 2006 with corrections to the Cover Date.     

Using sticker model of DNA computing to solve domatic partition, kernel and induced path problems

DNA computing as a powerful interdisciplinary field has been found to be very useful and applicable for solving NP-complete and intractable problems because of its huge power in parallel processing. In recent years many efforts have been done to solve NP-complete and time consuming problems with the help of DNA computing. In this paper, we use sticker model (one of the most well-known models of DNA computing) to present three DNA algorithms for solving three different NP-complete graph-based problems for the first time: domatic partition, kernel and induced path. Also we have simulated these algorithms to show their correctness.     

基于粘贴系统的有向哈密顿路问题分析

通过构造粘贴模型模拟解决有向哈密顿路问题,然后用此粘贴系统所产生语言的性质对有向哈密顿路问题进行分析,继而给出了有向哈密顿路的充要条件。对于规模为n有向哈密顿路问题,构造的粘贴系统至多运行n-1步。     

Efficient DNA sticker algorithms for NP-complete graph problems

Adleman's successful solution of a seven-vertex instance of the NP-complete Hamiltonian directed path problem by a DNA algorithm initiated the field of biomolecular computing. We provide DNA algorithms based on the sticker model to compute all k-cliques, independent k-sets, Hamiltonian paths, and Steiner trees with respect to a given edge or vertex set. The algorithms determine not merely the existence of a solution but yield all solutions (if any). For an undirected graph with n vertices and m edges, the running time of the algorithms is linear in n+m. For this, the sticker algorithms make use of small combinatorial input libraries instead of commonly used large libraries. The described algorithms are entirely theoretical in nature. They may become very useful in practice, when further advances in biotechnology lead to an efficient implementation of the sticker model.     

Improved DNA-sticker arithmetic: tube-encoded-carry, Logarithmic Number System and Monte-Carlo methods

The sticker model of computation, implemented using robotic processing of DNA, manipulates in parallel many bitstrings, called strands, that are contained in a limited number of tubes. Prior sticker arithmetic algorithms, patterned on digital-electronics, generate carry bits in the strand, either wasting bits or using a clear operation (with problematic biochemical implementation). The novel addition algorithm here does not need to record the carry. Instead, which tube holds a particular strand implicitly encodes the carry. The speed and number of tubes are half that of prior approaches. Further encoding data in the Logarithmic Number System (LNS) allows such integer operations to perform cost-effective real multiplications, divisions and roots. An example LNS Euclidian norm is more efficient than prior methods, assuming perfect operations. Unfortunately, DNA-stickers are unreliable. This paper uses sticker unreliability as a source of randomness to implement Monte-Carlo (MC) arithmetic (previously fabricated in silicon at the cost of pseudo-random generators). With stickers, the randomness is free. MC engineering mimics natural systems using unreliable but redundant components. Here, MC randomness is only useful in low-order bits. Multiple re-testing of the same bit (“refinement”) trades improved reliability for slower operation using more tubes. Simulations (with different sizes, probabilities and refinement) show that increasing refinement as a function of bit position allows imperfect implementations to achieve suitable MC strand-error distributions, predicting 1000x speed-mass advantage of sticker-MCLNS over conventional supercomputers.     

陶瓷烧结墨粉的研究与应用

本研究是使用可烧结的耐高温颜料代替普通墨粉中的色调剂制造一种特殊用途的墨粉,通过彩色激光打印机将所需要的图像直接打印到专用陶瓷烧结贴膜纸上,并将其直接粘到陶瓷承印物上,经高温烧结后,制造出各种陶瓷艺术品。     

计算科学的新领域：DNA计算（Ⅱ）

DNA计算是应用分子生物技术进行计算的新方法。从理论上研究DNA计算方法，有利于推动理论计算科学的发展。本系列文章应用形式语言及自动机理论技术，系统地探讨了DNA分子的可计算性及其计算能力。本文主要介绍DNA分子粘接计算模型的文法结构和计算方法，探讨了不同粘接计算模型的计算能力，并证明了DNA有穷自动机与正规文法的等价性。     

一类禁位排列问题的粘贴DNA算法

提出了广义的分离操作和广义的多级分离操作的概念,简要说明了二者的区别,并给出了其实现方法。基于粘贴模型的巨大并行性,给出了一类禁位排列问题的粘贴DNA算法,分别使用扩展的分离操作和扩展的多级分离操作实现了该算法。通过一个实例说明了给出的实验操作步骤,并对生化实验进行了模拟,得出了模拟结果,从而证明了该算法的可行性。最后,对算法的操作复杂度进行了分析。     

Reversible anemometric sticker sensor applied on finalized polymeric LoC devices

In this paper, an anemometric sticker sensor is presented, which can be used as a flag to verify the completion of a particular step inside microfluidic devices, the presence of leakages or trapped air bubbles. The similarity of the fabrication method to the printing and roll-to-roll techniques offers a simple and realistic mass-producible solution for direct monitoring of microfluidic protocols inside lab-on-a-chip devices. The detector has been fabricated on a sticker, which presents low space needs and can be easily applied on the test chip with no strict alignment requirements. The introduced idea fulfills the sensing demand that currently microfluidic devices present, being reusable or disposable due to its low cost requirements.     

Fair sticker languages

Codings of fair sticker languages are characterized as languages accepted by blind one-counter automata. Received 17 March 2000     

Arithmetic Complexity, Kleene Closure, and Formal Power Series

The aim of this paper is to use formal power series techniques to study the structure of small arithmetic complexity classes such as GapNC ¹ and GapL. More precisely, we apply the formal power series operations of inversion and root extraction to these complexity classes. We define a counting version of Kleene closure and show that it is intimately related to inversion and root extraction within GapNC ¹ and GapL. We prove that Kleene closure, inversion, and root extraction are all hard operations in the following sense: there is a language in AC ⁰ for which inversion and root extraction are GapL-complete and Kleene closure is NLOG-complete, and there is a finite set for which inversion and root extraction are GapNC ¹ -complete and Kleene closure is NC ¹ -complete, with respect to appropriate reducibilities. The latter result raises the question of classifying finite languages so that their inverses fall within interesting subclasses of GapNC ¹ , such as GapAC ⁰ . We initiate work in this direction by classifying the complexity of the Kleene closure of finite languages. We formulate the problem in terms of finite monoids and relate its complexity to the internal structure of the monoid. Some results in this paper show properties of complexity classes that are interesting independent of formal power series considerations, including some useful closure properties and complete problems for GapL.     

对抗彩色贴片：一种针对DNNs的对抗攻击手段

深度神经网络（deep neural networks,DNNs）在图像分类、分割、物体检测等计算机视觉应用方面表现出了先进的性能。然而,最近的研究进展表明,DNNs很容易受到输入数据的人工数字扰动（即对抗性攻击）的干扰。深度神经网络的分类准确率受到其训练数据集的数据分布的显著影响,而输入图像的颜色空间受到扭曲或扰动会产生分布不均匀的数据,这使深度神经网络更容易对它们进行错误分类。提出了一种简单且高效的攻击手段——对抗彩色贴片（AdvCS）,利用粒子群优化算法优化彩色贴片的物理参数,实现物理环境下的有效攻击。首先,提出了一个图片背景颜色变化的数据集,通过在ImageNet的一个子集上用27个不同的组合改变他们的RGB通道颜色,研究颜色变化对DNNs性能的影响。在提出的数据集上对几种最先进的DNNs架构进行了实验,结果显示颜色变化和分类准确率损失之间存在显著相关性。此外,基于ResNet 50架构,在提出的数据集上演示了最近提出的鲁棒训练技术和策略（如Augmix、Revisiting、Normalizer Free）的一些性能实验。实验结果表明,这些鲁棒训练技术可以提高深度神经网络对颜色变化的鲁棒性。然后,使用彩色半透明贴片作为物理扰动,利用粒子群优化算法优化其物理参数,将其置于摄像头上执行物理攻击,实验结果验证了提出的方法的有效性。     

甲骨文检索的粘贴DNA算法

为了能更好地研究和保护甲骨文,设计了一种适合DNA计算机的甲骨文编码方式,并据此提出了进行甲骨文检索的粘贴DNA算法。根据DNA双链分子具有双螺旋结构的特性,甲骨文标准字库的编码和待检索文字的编码采用了互补的方式,以利于生化操作的执行。仿真结果表明该算法具有可行性和有效性。     

有向图k顶点导出子图的DNA粘贴算法

在经典的电子计算中,有向图k顶点导出子图是一个高度复杂的问题。DNA计算是近年来发展的以DNA为载体求解计算问题的非经典计算技术。文中研究了使用DNA计算解决有向图k顶点导出子图的问题,从而提出了一种在粘贴机上运行的子图生成算法。首先,以粘贴机的标准生化元操作作为算法调用的基本算子;其次,使用顺序与循环等程序结构,把上述基本算子按照一定的逻辑方式组织起来;最后,读取生化反应结果,即可获得给定有向图的所有k顶点导出子图。仿真实验结果表明,与经典算法相比,新算法在理想条件下大幅缩短了子图生成时间。     

图的最大团与最大独立集粘贴DNA计算模型

粘贴模型(stickermodel)是DNA计算中一个很重要的模型.其主要原理就是采用单双链混合型DNA分子进行编码,其优点在于在生物操作过程中不需要DNA链的延伸,不需要生物酶的作用以及DNA链可重复使用等,因此引起了来自不同学科的学者们的广泛关注与兴趣.文中提出了一种求解图的最大团问题的DNA计算模型,该模型采用了两种基本并行计算处理思想,一种是将图分解成小的子图来处理的并行思想;另一种是进行并行生物操作.     

Nonerasing, Counting, and Majority over the Linear Time Hierarchy

In this paper, we investigate several extensions of the linear time hierarchy (denoted by LTH). We first prove that it is not necessary to erase the oracle tape between two successive oracle calls, thereby lifting a common restriction on LTH machines. We also define a natural counting extension of LTH and show that it corresponds to a robust notion of counting bounded arithmetic predicates. Finally, we show that the computational power of the majority operator is equivalent to that of the exact counting operator in both contexts.     

DNA分子计算模型

The field of practical DNA computing opened in 1994 with Adleman's paper,in which a laboratory experi-ment involving DNA molecules was used to solve a small instance of the Hamiltonian Path problem. The characteris-tic of this computation is its powerful ability in parallelism,its huge storage and high energy efficiency. This paper mainly introduces the principles of DNA computing and the sticker computing model.     

On the Power of Las Vegas for One-Way Communication Complexity, OBDDs, and Finite Automata

The study of the computational power of randomized computations is one of the central tasks of complexity theory. The main goal of this paper is the comparison of the power of Las Vegas computation and deterministic respectively nondeterministic computation. We investigate the power of Las Vegas computation for the complexity measures of one-way communication, ordered binary decision diagrams, and finite automata.(i) For the one-way communication complexity of two-party protocols we show that Las Vegas communication can save at most one half of the deterministic one-way communication complexity. We also present a language for which this gap is tight.(ii) The result (i) is applied to show an at most polynomial gap between determinism and Las Vegas for ordered binary decision diagrams.(iii) For the size (i.e., the number of states) of finite automata we show that the size of Las Vegas finite automata recognizing a language L is at least the square root of the size of the minimal deterministic finite automaton recognizing L. Using a specific language we verify the optimality of this lower bound.     

Adaptive scanning, 1‐D dimming,and boosting backlight for LCD‐TV systems

Abstract— Because TV applications require proper motion portrayal, overdrive and impulse driving are both required. Advanced lamp control enables Scanning Backlight Technology to drive the LCD panel with a pulsed exposure. Adaptive Dual‐Pulse Technology can be applied to eliminate the induced image flicker. Light leaking through LCD panels driven to black can be described as a poor black level, limiting the contrast ratio. Adaptive Dimming Technology can be applied to dim the backlight, while maintaining image quality and saving power. The limited transmittance of LCD panels can be described as weak brightness. The transmission of the LCD panel should be maximized and Adaptive Boosting Technology can be used to boost the backlight (>100%). When combining these technologies, motion portrayal is enhanced, local brightness may double, and the contrast may be increased up to a factor of 20, still saving power.